paired end

marine.py

@@ -218,8 +218,13 @@ def generate_depths(output_folder, bam_filepaths, paired_end=False, barcode_tag=
                                   all_depth_commands=all_depth_commands, output_suffix='source_cells', run=True, processes=cores, barcode_tag=barcode_tag)
 
     else:
+        if paired_end:
+            paired_end_flag = '-s '
+        else:
+            paired_end_flag = 's'
+
         # Bulk mode, we will not split the bed and simply use samtools depth on the combined.bed
-        samtools_depth_command = f"samtools depth -b {output_folder}/combined_source_cells.bed {bam_filepath} > {output_folder}/depths_source_cells.txt"
+        samtools_depth_command = f"samtools depth {paired_end_flag}-a -b {output_folder}/combined_source_cells.bed {bam_filepath} > {output_folder}/depths_source_cells.txt"
         run_command(samtools_depth_command)
 
 

tests/integration_tests.ipynb

@@ -2889,7 +2889,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 1,
    "id": "f5c3ed3e-13dd-4399-924e-3d1ac17ce387",
    "metadata": {},
    "outputs": [
@@ -3021,10 +3021,11 @@
       "\t >>> long_read_sc_test passed! <<<\n",
       "\n",
       "Checking that analyzing a single-cell dataset in 'bulk' mode (i.e. not specificying the 'CB' barcode) yields the exact same positions and base changes, but with counts and coverages aggregated rather than at a single-cell resolution\n",
+      "Exception: \n",
       "\n",
-      "\t >>> single-cell and bulk on same dataset comparison passed! <<<\n",
+      "\t ~~~ single cell vs bulk modes on sc dataset equivalency test FAILED! ~~~\n",
       "\n",
-      "There were 3 failures\n"
+      "There were 4 failures\n"
      ]
     }
    ],